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Job request: 19532

Organisation:
Bennett Institute
Workspace:
isaric-translation
ID:
ipmiyhxbxsoncd3n
View repo View project.yaml

This page shows the technical details of what happened when the authorised researcher Millie Green requested one or more actions to be run against real patient data in the project, within a secure environment.

By cross-referencing the list of jobs with the pipeline section below, you can infer what security level various outputs were written to. Researchers can never directly view outputs marked as highly_sensitive ; they can only request that code runs against them. Outputs marked as moderately_sensitive can be viewed by an approved researcher by logging into a highly secure environment. Only outputs marked as moderately_sensitive can be requested for release to the public, via a controlled output review service.

Jobs

Pipeline

Show project.yaml 
version: '3.0'

expectations:

  population_size: 1000

actions:

  ## # # # # # # # # # # # # # # # # # # #
  ## DO NOT EDIT project.yaml DIRECTLY
  ## This file is created by create-project.R
  ## Edit and run create-project.R to update the project.yaml
  ## # # # # # # # # # # # # # # # # # # #
  ## # # # # # # # # # # # # # # # # # # #
  ## Extract admission date
  ## # # # # # # # # # # # # # # # # # # #

  extract_isaric_admission1:
    run: databuilder:v0 generate-dataset 'analysis/dataset_definition_isaric.py' --dummy-tables
      'dummy-tables/' --output 'output/admissions/isaric_admission1.csv.gz'
    needs: []
    outputs:
      highly_sensitive:
        csv: output/admissions/isaric_admission1.csv.gz

  data_properties:
    run: r:latest analysis/data_properties.R output/admissions/isaric_admission1.csv.gz output/data_properties
    needs: [extract_isaric_admission1]
    outputs:
      moderately_sensitive:
        cohort: output/data_properties/isaric_admission1*.txt

  process_isaric:
    run: r:latest analysis/process_isaric.R
    needs:
    - extract_isaric_admission1
    outputs:
      highly_sensitive:
        rds: output/admissions/processed_isaric.rds
      moderately_sensitive:
        txt: output/admissions/isaric_raw_skim.txt

  extract_sus_methodA_admission1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodA_admission1.csv.gz --param admission_number=1
      --param admission_method=A
    needs: []
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodA_admission1.csv.gz

  extract_sus_methodA_admission2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodA_admission2.csv.gz --param admission_number=2
      --param admission_method=A
    needs:
    - extract_sus_methodA_admission1
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodA_admission2.csv.gz

  extract_sus_methodA_admission3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodA_admission3.csv.gz --param admission_number=3
      --param admission_method=A
    needs:
    - extract_sus_methodA_admission2
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodA_admission3.csv.gz

  extract_sus_methodA_admission4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodA_admission4.csv.gz --param admission_number=4
      --param admission_method=A
    needs:
    - extract_sus_methodA_admission3
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodA_admission4.csv.gz

  extract_sus_methodA_admission5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodA_admission5.csv.gz --param admission_number=5
      --param admission_method=A
    needs:
    - extract_sus_methodA_admission4
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodA_admission5.csv.gz

  extract_sus_methodB_admission1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodB_admission1.csv.gz --param admission_number=1
      --param admission_method=B
    needs: []
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodB_admission1.csv.gz

  extract_sus_methodB_admission2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodB_admission2.csv.gz --param admission_number=2
      --param admission_method=B
    needs:
    - extract_sus_methodB_admission1
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodB_admission2.csv.gz

  extract_sus_methodB_admission3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodB_admission3.csv.gz --param admission_number=3
      --param admission_method=B
    needs:
    - extract_sus_methodB_admission2
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodB_admission3.csv.gz

  extract_sus_methodB_admission4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodB_admission4.csv.gz --param admission_number=4
      --param admission_method=B
    needs:
    - extract_sus_methodB_admission3
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodB_admission4.csv.gz

  extract_sus_methodB_admission5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodB_admission5.csv.gz --param admission_number=5
      --param admission_method=B
    needs:
    - extract_sus_methodB_admission4
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodB_admission5.csv.gz

  extract_sus_methodC_admission1:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodC_admission1.csv.gz --param admission_number=1
      --param admission_method=C
    needs: []
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodC_admission1.csv.gz

  extract_sus_methodC_admission2:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodC_admission2.csv.gz --param admission_number=2
      --param admission_method=C
    needs:
    - extract_sus_methodC_admission1
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodC_admission2.csv.gz

  extract_sus_methodC_admission3:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodC_admission3.csv.gz --param admission_number=3
      --param admission_method=C
    needs:
    - extract_sus_methodC_admission2
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodC_admission3.csv.gz

  extract_sus_methodC_admission4:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodC_admission4.csv.gz --param admission_number=4
      --param admission_method=C
    needs:
    - extract_sus_methodC_admission3
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodC_admission4.csv.gz

  extract_sus_methodC_admission5:
    run: cohortextractor:latest generate_cohort --study-definition study_definition_sus
      --output-file output/admissions/sus_methodC_admission5.csv.gz --param admission_number=5
      --param admission_method=C
    needs:
    - extract_sus_methodC_admission4
    outputs:
      highly_sensitive:
        csv: output/admissions/sus_methodC_admission5.csv.gz

  process_sus:
    run: r:latest analysis/process_sus.R
    needs:
    - extract_sus_methodA_admission1
    - extract_sus_methodA_admission2
    - extract_sus_methodA_admission3
    - extract_sus_methodA_admission4
    - extract_sus_methodA_admission5
    - extract_sus_methodB_admission1
    - extract_sus_methodB_admission2
    - extract_sus_methodB_admission3
    - extract_sus_methodB_admission4
    - extract_sus_methodB_admission5
    - extract_sus_methodC_admission1
    - extract_sus_methodC_admission2
    - extract_sus_methodC_admission3
    - extract_sus_methodC_admission4
    - extract_sus_methodC_admission5
    outputs:
      highly_sensitive:
        rds: output/admissions/processed_sus*.rds

  validation_events:
    run: r:latest analysis/validation_events.R
    needs:
    - process_isaric
    - process_sus
    outputs:
      moderately_sensitive:
        csv: output/validation_events/*.csv

  validation_characteristics:
    run: r:latest analysis/validation_characteristics.R
    needs:
    - process_isaric
    - process_sus
    outputs:
      moderately_sensitive:
        csv: output/validation_characteristics/*.csv
        jpg: output/validation_characteristics/*.jpg

  ## # # # # # # # # # # # # # # # # # # #
  ## End
  ## # # # # # # # # # # # # # # # # # # #

Timeline

  • Created:

  • Started:

  • Finished:

  • Runtime: 00:03:16

These timestamps are generated and stored using the UTC timezone on the TPP backend.

Job information

Status
Succeeded
Backend
TPP
Workspace
isaric-translation
Requested by
Millie Green
Branch
translation
Force run dependencies
No
Git commit hash
82784c7
Requested actions
  • data_properties

Code comparison

Compare the code used in this Job Request